Package Bio :: Package Blast :: Module Applications
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Source Code for Module Bio.Blast.Applications

  1  """Definitions for interacting with Blast related applications. 
  2  """ 
  3  from Bio import Application 
  4  from Bio.Application import _Option 
  5   
6 -class FastacmdCommandline(Application.AbstractCommandline):
7 """Create a commandline for the fasta program from NCBI. 8 9 """ 10
11 - def __init__(self, fastacmd = "fastacmd"):
12 Application.AbstractCommandline.__init__(self) 13 14 self.program_name = fastacmd 15 16 self.parameters = \ 17 [ 18 _Option(["-d", "database"], ["input"], None, 1, 19 "The database to retrieve from."), 20 _Option(["-s", "search_string"], ["input"], None, 1, 21 "The id to search for.") 22 ]
23
24 -class BlastallCommandline(Application.AbstractCommandline):
25 """Create a commandline for the blastall program from NCBI. 26 27 XXX This could use more checking for valid paramters to the program. 28 """
29 - def __init__(self, blastcmd = "blastall"):
30 Application.AbstractCommandline.__init__(self) 31 32 self.program_name = blastcmd 33 34 self.parameters = \ 35 [# Scoring options 36 _Option(["-M", "matrix"], ["input"], None, 0, 37 "Matrix to use"), 38 _Option(["-G", "gap_open"], ["input"], None, 0, 39 "Gap open penalty"), 40 _Option(["-E", "gap_extend"], ["input"], None, 0, 41 "Gap extension penalty"), 42 _Option(["-A", "window_size"], ["input"], None, 0, 43 "Multiple hits window size"), 44 _Option(["-j", "npasses"], ["input"], None, 0, 45 "Number of passes"), 46 _Option(["-p", "passes"], ["input"], None, 0, 47 "Hits/passes. Integer 0-2."), 48 49 # Algorithm options 50 _Option(["-g", "gapped"], ["input"], None, 0, 51 "Whether to do a gapped alignment. T/F"), 52 _Option(["-e", "expectation"], ["input"], None, 0, 53 "Expectation value cutoff."), 54 _Option(["-W", "wordsize"], ["input"], None, 0, 55 "Word size"), 56 _Option(["-K", "keep_hits"], ["input"], None, 0, 57 " Number of best hits from a region to keep."), 58 _Option(["-X", "xdrop"], ["input"], None, 0, 59 "Dropoff value (bits) for gapped alignments."), 60 _Option(["-f", "hit_extend"], ["input"], None, 0, 61 "Threshold for extending hits."), 62 _Option(["-L", "region_length"], ["input"], None, 0, 63 "Length of region used to judge hits."), 64 _Option(["-Z", "db_length"], ["input"], None, 0, 65 "Effective database length."), 66 _Option(["-Y", "search_length"], ["input"], None, 0, 67 "Effective length of search space."), 68 _Option(["-N", "nbits_gapping"], ["input"], None, 0, 69 "Number of bits to trigger gapping."), 70 _Option(["-c", "pseudocounts"], ["input"], None, 0, 71 "Pseudocounts constants for multiple passes."), 72 _Option(["-Z", "xdrop_final"], ["input"], None, 0, 73 "X dropoff for final gapped alignment."), 74 _Option(["-y", "xdrop_extension"], ["input"], None, 0, 75 "Dropoff for blast extensions."), 76 _Option(["-h", "model_threshold"], ["input"], None, 0, 77 "E-value threshold to include in multipass model."), 78 _Option(["-S", "required_start"], ["input"], None, 0, 79 "Start of required region in query."), 80 _Option(["-H", "required_end"], ["input"], None, 0, 81 "End of required region in query."), 82 83 # Processing options 84 _Option(["-p", "program"], ["input"], None, 1, 85 "The blast program to use."), 86 _Option(["-d", "database"], ["input"], None, 1, 87 "The database to BLAST against."), 88 _Option(["-i", "infile"], ["input", "file"], None, 1, 89 "The sequence to search with."), 90 _Option(["-F", "filter"], ["input"], None, 0, 91 "Filter query sequence with SEG? T/F"), 92 _Option(["-J", "believe_query"], ["input"], None, 0, 93 "Believe the query defline? T/F"), 94 _Option(["-a", "nprocessors"], ["input"], None, 0, 95 "Number of processors to use."), 96 97 # Formatting options 98 _Option(["-T", "html"], ["input"], None, 0, 99 "Produce HTML output? T/F"), 100 _Option(["-v", "descriptions"], ["input"], None, 0, 101 "Number of one-line descriptions."), 102 _Option(["-b", "alignments"], ["input"], None, 0, 103 "Number of alignments."), 104 _Option(["-m", "align_view"], ["input"], None, 0, 105 "Alignment view. Integer 0-6."), 106 _Option(["-I", "show_gi"], ["input"], None, 0, 107 "Show GI's in deflines? T/F"), 108 _Option(["-O", "seqalign_file"], ["output", "file"], None, 0, 109 "seqalign file to output."), 110 _Option(["-o", "align_outfile"], ["output", "file"], None, 1, 111 "Output file for alignment."), 112 _Option(["-C", "checkpoint_outfile"], ["output", "file"], None, 0, 113 "Output file for PSI-BLAST checkpointing."), 114 _Option(["-R", "restart_infile"], ["input", "file"], None, 0, 115 "Input file for PSI-BLAST restart."), 116 _Option(["-k", "hit_infile"], ["input", "file"], None, 0, 117 "Hit file for PHI-BLAST."), 118 _Option(["-Q", "matrix_outfile"], ["output", "file"], None, 0, 119 "Output file for PSI-BLAST matrix in ASCII."), 120 _Option(["-B", "align_infile"], ["input", "file"], None, 0, 121 "Input alignment file for PSI-BLAST restart.") 122 ]
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